Starting phenix.real_space_refine on Tue Feb 3 13:20:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s15_24794/02_2026/7s15_24794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s15_24794/02_2026/7s15_24794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s15_24794/02_2026/7s15_24794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s15_24794/02_2026/7s15_24794.map" model { file = "/net/cci-nas-00/data/ceres_data/7s15_24794/02_2026/7s15_24794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s15_24794/02_2026/7s15_24794.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.060 sd= 0.638 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2117 2.51 5 N 525 2.21 5 O 545 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3207 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3164 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 2 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'82L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.93, per 1000 atoms: 0.29 Number of scatterers: 3207 At special positions: 0 Unit cell: (65.296, 65.296, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 F 2 9.00 O 545 8.00 N 525 7.00 C 2117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.05 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 121.0 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 66.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'R' and resid 31 through 52 removed outlier: 3.649A pdb=" N ARG R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 138 through 166 removed outlier: 4.021A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 202 removed outlier: 3.925A pdb=" N ALA R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 221 Processing helix chain 'R' and resid 225 through 254 removed outlier: 3.698A pdb=" N TYR R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 244 " --> pdb=" O ASN R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.518A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 280 Processing helix chain 'R' and resid 281 through 292 removed outlier: 4.083A pdb=" N LEU R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 335 removed outlier: 4.182A pdb=" N ARG R 310 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 360 removed outlier: 4.333A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER R 352 " --> pdb=" O ARG R 348 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 removed outlier: 3.894A pdb=" N PHE R 367 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 393 removed outlier: 4.098A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 404 removed outlier: 3.932A pdb=" N VAL R 398 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE R 404 " --> pdb=" O ILE R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.663A pdb=" N GLN R 410 " --> pdb=" O ASN R 406 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 972 1.34 - 1.46: 936 1.46 - 1.58: 1378 1.58 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 3309 Sorted by residual: bond pdb=" C41 82L R 501 " pdb=" O43 82L R 501 " ideal model delta sigma weight residual 1.259 1.303 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C12 82L R 501 " pdb=" C41 82L R 501 " ideal model delta sigma weight residual 1.527 1.485 0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C41 82L R 501 " pdb=" O42 82L R 501 " ideal model delta sigma weight residual 1.258 1.222 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA GLN R 394 " pdb=" C GLN R 394 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.80e-02 3.09e+03 1.97e+00 bond pdb=" C1 82L R 501 " pdb=" C2 82L R 501 " ideal model delta sigma weight residual 1.523 1.498 0.025 2.00e-02 2.50e+03 1.59e+00 ... (remaining 3304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 4207 1.49 - 2.98: 253 2.98 - 4.47: 37 4.47 - 5.96: 10 5.96 - 7.45: 4 Bond angle restraints: 4511 Sorted by residual: angle pdb=" CA LEU R 166 " pdb=" C LEU R 166 " pdb=" N LEU R 167 " ideal model delta sigma weight residual 118.27 123.59 -5.32 1.59e+00 3.96e-01 1.12e+01 angle pdb=" CA CYS R 126 " pdb=" CB CYS R 126 " pdb=" SG CYS R 126 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.92 117.03 4.89 1.73e+00 3.34e-01 7.99e+00 angle pdb=" N THR R 65 " pdb=" CA THR R 65 " pdb=" C THR R 65 " ideal model delta sigma weight residual 108.34 111.87 -3.53 1.31e+00 5.83e-01 7.27e+00 angle pdb=" CA TYR R 145 " pdb=" CB TYR R 145 " pdb=" CG TYR R 145 " ideal model delta sigma weight residual 113.90 109.74 4.16 1.80e+00 3.09e-01 5.34e+00 ... (remaining 4506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1635 16.43 - 32.86: 209 32.86 - 49.30: 59 49.30 - 65.73: 9 65.73 - 82.16: 5 Dihedral angle restraints: 1917 sinusoidal: 786 harmonic: 1131 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -14.81 -71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 153.24 -60.24 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CA CYS R 296 " pdb=" C CYS R 296 " pdb=" N TRP R 297 " pdb=" CA TRP R 297 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 1914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 272 0.034 - 0.069: 150 0.069 - 0.103: 49 0.103 - 0.137: 14 0.137 - 0.171: 1 Chirality restraints: 486 Sorted by residual: chirality pdb=" C22 82L R 501 " pdb=" C21 82L R 501 " pdb=" C23 82L R 501 " pdb=" C25 82L R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CG LEU R 218 " pdb=" CB LEU R 218 " pdb=" CD1 LEU R 218 " pdb=" CD2 LEU R 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA GLN R 394 " pdb=" N GLN R 394 " pdb=" C GLN R 394 " pdb=" CB GLN R 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 483 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 82L R 501 " 0.315 2.00e-02 2.50e+03 1.43e-01 4.59e+02 pdb=" C33 82L R 501 " -0.165 2.00e-02 2.50e+03 pdb=" C34 82L R 501 " -0.149 2.00e-02 2.50e+03 pdb=" C35 82L R 501 " -0.048 2.00e-02 2.50e+03 pdb=" C36 82L R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C37 82L R 501 " 0.022 2.00e-02 2.50e+03 pdb=" C38 82L R 501 " -0.078 2.00e-02 2.50e+03 pdb=" F39 82L R 501 " -0.074 2.00e-02 2.50e+03 pdb=" F40 82L R 501 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 82L R 501 " -0.066 2.00e-02 2.50e+03 3.87e-02 3.00e+01 pdb=" C25 82L R 501 " 0.041 2.00e-02 2.50e+03 pdb=" C26 82L R 501 " 0.021 2.00e-02 2.50e+03 pdb=" C27 82L R 501 " -0.014 2.00e-02 2.50e+03 pdb=" C28 82L R 501 " -0.025 2.00e-02 2.50e+03 pdb=" C29 82L R 501 " 0.015 2.00e-02 2.50e+03 pdb=" N30 82L R 501 " 0.059 2.00e-02 2.50e+03 pdb=" O31 82L R 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 82L R 501 " 0.022 2.00e-02 2.50e+03 2.15e-02 1.39e+01 pdb=" C11 82L R 501 " 0.013 2.00e-02 2.50e+03 pdb=" C12 82L R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C13 82L R 501 " -0.026 2.00e-02 2.50e+03 pdb=" C14 82L R 501 " -0.007 2.00e-02 2.50e+03 pdb=" C15 82L R 501 " 0.019 2.00e-02 2.50e+03 pdb=" C17 82L R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C18 82L R 501 " -0.049 2.00e-02 2.50e+03 pdb=" C41 82L R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C8 82L R 501 " -0.011 2.00e-02 2.50e+03 pdb=" N16 82L R 501 " 0.022 2.00e-02 2.50e+03 pdb=" N9 82L R 501 " 0.017 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 204 2.72 - 3.26: 3555 3.26 - 3.81: 5083 3.81 - 4.35: 5892 4.35 - 4.90: 9473 Nonbonded interactions: 24207 Sorted by model distance: nonbonded pdb=" OH TYR R 241 " pdb=" OE2 GLU R 364 " model vdw 2.174 3.040 nonbonded pdb=" O GLN R 47 " pdb=" OG1 THR R 51 " model vdw 2.276 3.040 nonbonded pdb=" O THR R 386 " pdb=" OG SER R 389 " model vdw 2.293 3.040 nonbonded pdb=" O LEU R 349 " pdb=" OG SER R 352 " model vdw 2.317 3.040 nonbonded pdb=" OD1 ASN R 304 " pdb=" NE1 TRP R 306 " model vdw 2.326 3.120 ... (remaining 24202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3313 Z= 0.276 Angle : 0.812 7.447 4519 Z= 0.443 Chirality : 0.046 0.171 486 Planarity : 0.008 0.143 551 Dihedral : 15.907 82.158 1173 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.35), residues: 376 helix: -2.23 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -4.38 (0.42), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 64 TYR 0.015 0.002 TYR R 145 PHE 0.016 0.002 PHE R 143 TRP 0.028 0.002 TRP R 297 HIS 0.003 0.001 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 3309) covalent geometry : angle 0.80924 ( 4511) SS BOND : bond 0.01017 ( 4) SS BOND : angle 1.70485 ( 8) hydrogen bonds : bond 0.13309 ( 162) hydrogen bonds : angle 5.81600 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 244 LEU cc_start: 0.9032 (mp) cc_final: 0.8820 (mp) REVERT: R 269 TYR cc_start: 0.8017 (m-10) cc_final: 0.7458 (m-80) REVERT: R 394 GLN cc_start: 0.9370 (pp30) cc_final: 0.8430 (pp30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0728 time to fit residues: 8.3005 Evaluate side-chains 66 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.124938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.109267 restraints weight = 8765.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112393 restraints weight = 4494.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.114434 restraints weight = 2709.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115866 restraints weight = 1822.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116739 restraints weight = 1325.788| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3313 Z= 0.149 Angle : 0.716 6.971 4519 Z= 0.359 Chirality : 0.042 0.156 486 Planarity : 0.004 0.044 551 Dihedral : 6.146 28.210 455 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.91 % Favored : 92.82 % Rotamer: Outliers : 2.92 % Allowed : 17.84 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.42), residues: 376 helix: -0.65 (0.33), residues: 248 sheet: None (None), residues: 0 loop : -3.49 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 310 TYR 0.017 0.002 TYR R 235 PHE 0.011 0.001 PHE R 315 TRP 0.025 0.002 TRP R 297 HIS 0.003 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3309) covalent geometry : angle 0.71384 ( 4511) SS BOND : bond 0.00726 ( 4) SS BOND : angle 1.55157 ( 8) hydrogen bonds : bond 0.04785 ( 162) hydrogen bonds : angle 4.24148 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9055 (mp0) cc_final: 0.8805 (mp0) REVERT: R 68 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8331 (mm-30) REVERT: R 198 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.7877 (t0) REVERT: R 234 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8899 (mm110) REVERT: R 394 GLN cc_start: 0.9095 (pp30) cc_final: 0.8827 (pp30) REVERT: R 404 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5612 (m-80) outliers start: 10 outliers final: 4 residues processed: 86 average time/residue: 0.0546 time to fit residues: 5.9682 Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 HIS R 211 GLN R 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111907 restraints weight = 8668.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115145 restraints weight = 4413.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117230 restraints weight = 2640.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118655 restraints weight = 1763.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119551 restraints weight = 1267.027| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3313 Z= 0.114 Angle : 0.633 6.484 4519 Z= 0.314 Chirality : 0.039 0.113 486 Planarity : 0.004 0.046 551 Dihedral : 5.759 28.143 455 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.22 % Allowed : 23.68 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.44), residues: 376 helix: 0.12 (0.34), residues: 247 sheet: None (None), residues: 0 loop : -2.95 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 310 TYR 0.024 0.002 TYR R 148 PHE 0.009 0.001 PHE R 315 TRP 0.018 0.001 TRP R 297 HIS 0.002 0.001 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3309) covalent geometry : angle 0.62961 ( 4511) SS BOND : bond 0.00585 ( 4) SS BOND : angle 1.70290 ( 8) hydrogen bonds : bond 0.04185 ( 162) hydrogen bonds : angle 3.67003 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 GLU cc_start: 0.8993 (mp0) cc_final: 0.8656 (mp0) REVERT: R 68 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8292 (mm-30) REVERT: R 198 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8559 (t0) REVERT: R 394 GLN cc_start: 0.9035 (pp30) cc_final: 0.8726 (pp30) REVERT: R 404 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5646 (m-80) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.0508 time to fit residues: 5.6293 Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 17 optimal weight: 0.0870 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114937 restraints weight = 8279.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118222 restraints weight = 4260.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.120302 restraints weight = 2573.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121748 restraints weight = 1729.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122645 restraints weight = 1254.885| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3313 Z= 0.115 Angle : 0.609 6.310 4519 Z= 0.299 Chirality : 0.038 0.116 486 Planarity : 0.004 0.056 551 Dihedral : 5.343 26.714 455 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.22 % Allowed : 24.85 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.45), residues: 376 helix: 0.36 (0.34), residues: 248 sheet: None (None), residues: 0 loop : -2.65 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 310 TYR 0.014 0.002 TYR R 145 PHE 0.011 0.001 PHE R 280 TRP 0.017 0.001 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3309) covalent geometry : angle 0.60777 ( 4511) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.08616 ( 8) hydrogen bonds : bond 0.03798 ( 162) hydrogen bonds : angle 3.41712 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 GLU cc_start: 0.8987 (mp0) cc_final: 0.8725 (mp0) REVERT: R 68 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8432 (mm-30) REVERT: R 404 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5668 (m-80) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 0.0411 time to fit residues: 4.5989 Evaluate side-chains 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109285 restraints weight = 8779.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112314 restraints weight = 4513.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114290 restraints weight = 2736.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115648 restraints weight = 1856.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116569 restraints weight = 1361.764| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3313 Z= 0.183 Angle : 0.678 6.437 4519 Z= 0.338 Chirality : 0.042 0.146 486 Planarity : 0.005 0.061 551 Dihedral : 5.563 28.999 455 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.97 % Allowed : 26.32 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.45), residues: 376 helix: 0.35 (0.34), residues: 248 sheet: -3.26 (1.77), residues: 12 loop : -2.64 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 170 TYR 0.025 0.002 TYR R 269 PHE 0.011 0.002 PHE R 367 TRP 0.014 0.002 TRP R 243 HIS 0.004 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3309) covalent geometry : angle 0.67734 ( 4511) SS BOND : bond 0.00574 ( 4) SS BOND : angle 1.02731 ( 8) hydrogen bonds : bond 0.04274 ( 162) hydrogen bonds : angle 3.90602 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9007 (mp0) cc_final: 0.8566 (mp0) REVERT: R 68 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8642 (mm-30) REVERT: R 288 LYS cc_start: 0.8879 (tppt) cc_final: 0.8667 (tppp) REVERT: R 394 GLN cc_start: 0.9263 (pp30) cc_final: 0.8395 (pp30) REVERT: R 404 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.5676 (m-80) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.0398 time to fit residues: 3.9919 Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.129015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113343 restraints weight = 8435.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116499 restraints weight = 4350.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.118488 restraints weight = 2638.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119969 restraints weight = 1801.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.120962 restraints weight = 1310.818| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3313 Z= 0.114 Angle : 0.646 8.794 4519 Z= 0.308 Chirality : 0.040 0.118 486 Planarity : 0.004 0.063 551 Dihedral : 5.282 27.657 455 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.80 % Allowed : 28.07 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.45), residues: 376 helix: 0.48 (0.34), residues: 248 sheet: -2.96 (1.87), residues: 12 loop : -2.71 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 310 TYR 0.018 0.001 TYR R 148 PHE 0.010 0.001 PHE R 367 TRP 0.019 0.001 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3309) covalent geometry : angle 0.64518 ( 4511) SS BOND : bond 0.00425 ( 4) SS BOND : angle 0.91935 ( 8) hydrogen bonds : bond 0.03920 ( 162) hydrogen bonds : angle 3.49999 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.120 Fit side-chains REVERT: R 34 GLU cc_start: 0.9012 (mp0) cc_final: 0.8500 (mp0) REVERT: R 64 ARG cc_start: 0.6654 (ptp-170) cc_final: 0.6205 (ptp-170) REVERT: R 68 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8238 (mm-30) REVERT: R 394 GLN cc_start: 0.9192 (pp30) cc_final: 0.8309 (pp30) REVERT: R 404 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5678 (m-80) outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.0485 time to fit residues: 4.8617 Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.0050 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.128772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113028 restraints weight = 8787.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.116245 restraints weight = 4466.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118366 restraints weight = 2681.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119729 restraints weight = 1801.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.120659 restraints weight = 1320.179| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3313 Z= 0.111 Angle : 0.624 6.407 4519 Z= 0.303 Chirality : 0.039 0.117 486 Planarity : 0.005 0.066 551 Dihedral : 5.202 27.969 455 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.68 % Allowed : 27.19 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.45), residues: 376 helix: 0.52 (0.34), residues: 248 sheet: -2.67 (1.91), residues: 12 loop : -2.74 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 310 TYR 0.017 0.001 TYR R 145 PHE 0.010 0.001 PHE R 280 TRP 0.019 0.002 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3309) covalent geometry : angle 0.62301 ( 4511) SS BOND : bond 0.00463 ( 4) SS BOND : angle 0.89038 ( 8) hydrogen bonds : bond 0.03859 ( 162) hydrogen bonds : angle 3.47165 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.8924 (mp0) cc_final: 0.8512 (mp0) REVERT: R 394 GLN cc_start: 0.9194 (pp30) cc_final: 0.8300 (pp30) REVERT: R 404 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5711 (m-80) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.0428 time to fit residues: 4.2166 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111736 restraints weight = 8789.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114865 restraints weight = 4483.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.116918 restraints weight = 2687.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118224 restraints weight = 1804.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.119186 restraints weight = 1328.892| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.133 Angle : 0.638 6.298 4519 Z= 0.314 Chirality : 0.041 0.120 486 Planarity : 0.005 0.067 551 Dihedral : 6.162 49.914 455 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.68 % Allowed : 27.19 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.45), residues: 376 helix: 0.55 (0.34), residues: 248 sheet: -2.51 (1.87), residues: 12 loop : -2.79 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 170 TYR 0.016 0.001 TYR R 269 PHE 0.010 0.001 PHE R 230 TRP 0.018 0.002 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3309) covalent geometry : angle 0.63700 ( 4511) SS BOND : bond 0.00481 ( 4) SS BOND : angle 0.96064 ( 8) hydrogen bonds : bond 0.03978 ( 162) hydrogen bonds : angle 3.65688 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9016 (mp0) cc_final: 0.8488 (mp0) REVERT: R 68 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8512 (mm-30) REVERT: R 234 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8757 (mm-40) REVERT: R 394 GLN cc_start: 0.9220 (pp30) cc_final: 0.8307 (pp30) REVERT: R 404 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5739 (m-80) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.0283 time to fit residues: 2.9201 Evaluate side-chains 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114875 restraints weight = 8447.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118102 restraints weight = 4303.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.120220 restraints weight = 2585.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.121613 restraints weight = 1728.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122563 restraints weight = 1257.587| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3313 Z= 0.106 Angle : 0.635 8.162 4519 Z= 0.302 Chirality : 0.040 0.118 486 Planarity : 0.004 0.069 551 Dihedral : 7.056 75.468 455 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.09 % Allowed : 28.07 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.45), residues: 376 helix: 0.56 (0.34), residues: 251 sheet: -2.42 (1.85), residues: 12 loop : -2.81 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 310 TYR 0.013 0.001 TYR R 148 PHE 0.012 0.001 PHE R 280 TRP 0.021 0.001 TRP R 243 HIS 0.002 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3309) covalent geometry : angle 0.63426 ( 4511) SS BOND : bond 0.00404 ( 4) SS BOND : angle 0.96270 ( 8) hydrogen bonds : bond 0.03706 ( 162) hydrogen bonds : angle 3.49615 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.8979 (mp0) cc_final: 0.8540 (mp0) REVERT: R 68 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8408 (mm-30) REVERT: R 99 HIS cc_start: 0.7866 (m-70) cc_final: 0.7616 (m-70) REVERT: R 394 GLN cc_start: 0.9136 (pp30) cc_final: 0.8213 (pp30) REVERT: R 404 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5694 (m-80) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.0310 time to fit residues: 3.3362 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 33 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116231 restraints weight = 8372.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119427 restraints weight = 4234.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121554 restraints weight = 2552.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.122991 restraints weight = 1715.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123979 restraints weight = 1244.187| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3313 Z= 0.109 Angle : 0.634 7.548 4519 Z= 0.304 Chirality : 0.040 0.117 486 Planarity : 0.004 0.039 551 Dihedral : 6.649 70.703 455 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.92 % Allowed : 28.95 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.45), residues: 376 helix: 0.56 (0.34), residues: 250 sheet: -2.40 (1.86), residues: 12 loop : -2.78 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 310 TYR 0.008 0.001 TYR R 145 PHE 0.011 0.001 PHE R 280 TRP 0.020 0.001 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3309) covalent geometry : angle 0.63309 ( 4511) SS BOND : bond 0.00384 ( 4) SS BOND : angle 0.91360 ( 8) hydrogen bonds : bond 0.03622 ( 162) hydrogen bonds : angle 3.45297 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.8974 (mp0) cc_final: 0.8533 (mp0) REVERT: R 38 LYS cc_start: 0.9365 (tppt) cc_final: 0.8763 (tptt) REVERT: R 95 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7800 (m) REVERT: R 99 HIS cc_start: 0.7832 (m-70) cc_final: 0.7566 (m-70) REVERT: R 182 ASN cc_start: 0.9400 (t0) cc_final: 0.8592 (t0) REVERT: R 394 GLN cc_start: 0.9108 (pp30) cc_final: 0.8175 (pp30) REVERT: R 404 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5708 (m-80) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.0411 time to fit residues: 4.3516 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.110044 restraints weight = 8882.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.113170 restraints weight = 4463.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.115151 restraints weight = 2656.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116503 restraints weight = 1778.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117405 restraints weight = 1295.331| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3313 Z= 0.174 Angle : 0.697 8.139 4519 Z= 0.345 Chirality : 0.043 0.129 486 Planarity : 0.005 0.070 551 Dihedral : 7.562 83.506 455 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.92 % Allowed : 30.70 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.45), residues: 376 helix: 0.50 (0.34), residues: 250 sheet: -2.35 (1.85), residues: 12 loop : -2.74 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 170 TYR 0.011 0.002 TYR R 145 PHE 0.014 0.001 PHE R 230 TRP 0.018 0.002 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3309) covalent geometry : angle 0.69652 ( 4511) SS BOND : bond 0.00513 ( 4) SS BOND : angle 1.04302 ( 8) hydrogen bonds : bond 0.04197 ( 162) hydrogen bonds : angle 3.85625 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 631.26 seconds wall clock time: 11 minutes 29.62 seconds (689.62 seconds total)